GapMind for catabolism of small carbon sources

 

myo-inositol catabolism in Pseudomonas fluorescens FW300-N2E3

Best path

PS417_11885, PS417_11890, PS417_11895, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi

Also see fitness data for the top candidates

Rules

Overview: Myo-inositol degradation in GapMind is based on MetaCyc pathways myo-inositol degradation I via inosose dehydratase (link) and pathway II inosose dehydrogenase (link).

29 steps (19 with candidates)

Or see definitions of steps

Step Description Best candidate 2nd candidate
PS417_11885 myo-inositol ABC transporter, substrate-binding component AO353_21380
PS417_11890 myo-inositol ABC transporter, ATPase component AO353_21385 AO353_20820
PS417_11895 myo-inositol ABC transporter, permease component AO353_21390 AO353_20825
iolG myo-inositol 2-dehydrogenase AO353_21365 AO353_21490
iolE scyllo-inosose 2-dehydratase AO353_21340 AO353_23195
iolD 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione hydrolase AO353_21360
iolB 5-deoxy-D-glucuronate isomerase AO353_21345
iolC 5-dehydro-2-deoxy-D-gluconate kinase AO353_21335
iolJ 5-dehydro-2-deoxyphosphogluconate aldolase AO353_21335 AO353_07930
mmsA malonate-semialdehyde dehydrogenase AO353_21350 AO353_06080
tpi triose-phosphate isomerase AO353_05590 AO353_07945
Alternative steps:
eda 2-keto-3-deoxygluconate 6-phosphate aldolase AO353_03350 AO353_01265
HMIT myo-inositol:H+ symporter
iatA myo-inositol ABC transporter, ATPase component IatA AO353_21385 AO353_20820
iatP myo-inositol ABC transporter, permease component IatP AO353_21390 AO353_20825
ibpA myo-inositol ABC transporter, substrate-binding component IbpA
iolF myo-inositol:H+ symporter
iolM 2-inosose 4-dehydrogenase AO353_25145
iolN 2,4-diketo-inositol hydratase
iolO 5-dehydro-L-gluconate epimerase
iolT myo-inositol:H+ symporter
kdgK 2-keto-3-deoxygluconate kinase AO353_21745 AO353_26875
PGA1_c07300 myo-inositol ABC transport, substrate-binding component
PGA1_c07310 myo-inositol ABC transporter, permease component AO353_20825
PGA1_c07320 myo-inositol ABC transporter, ATPase component AO353_21385 AO353_20820
SMIT1 myo-inositol:Na+ symporter
uxaE D-tagaturonate epimerase
uxuA D-mannonate dehydratase
uxuB D-mannonate dehydrogenase AO353_25900

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory